BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716438.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 24,254,193 number of mapped reads = 23,654,904 (97.53%) number of supplementary alignments = 17,777 (0.07%) number of secondary alignments = 0 number of mapped bases = 1,604,749,488 bp number of sequenced bases = 1,604,470,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,177,752 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7334 >>>>>>> ACTG content number of A's = 443,374,868 bp (27.63%) number of C's = 355,986,361 bp (22.19%) number of T's = 465,239,882 bp (29%) number of G's = 339,630,049 bp (21.17%) number of N's = 239,644 bp (0.01%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 5,870,017 number of insertions = 137,240 mapped reads with insertion percentage = 0.58% number of deletions = 140,708 mapped reads with deletion percentage = 0.59% homopolymer indels = 35.87% >>>>>>> Coverage mean coverageData = 0.5184X std coverageData = 5.7018X There is a 36.26% of reference with a coverageData >= 1X There is a 9.78% of reference with a coverageData >= 2X There is a 2.31% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 154063836 0.6181081330184529 15.108832438043292 chr2 243199373 129214287 0.5313101156720499 3.5297561821990695 chr3 198022430 98247836 0.4961449872118022 2.0314848119701465 chr4 191154276 97521457 0.510171464853865 3.1670690158071766 chr5 180915260 90041015 0.497697181542342 0.8847986147077862 chr6 171115067 84724989 0.49513459267733567 1.583875000495078 chr7 159138663 83276300 0.5232939527712382 3.564934582407688 chr8 146364022 72797526 0.49737309077226644 2.2875963618212487 chr9 141213431 63956418 0.4529060553737272 2.0287757225503538 chr10 135534747 84559603 0.6238961216344028 11.941951371707997 chr11 135006516 89328463 0.6616603823773958 2.8616947360424656 chr12 133851895 68057711 0.5084553416296422 0.9698244383762145 chr13 115169878 51432467 0.4465791567479129 0.7865739081345658 chr14 107349540 45776636 0.42642600983665135 0.9438388935684903 chr15 102531392 45294304 0.4417603537460995 0.7495511696469022 chr16 90354753 44716319 0.4948972523891466 3.4106417166603626 chr17 81195210 56944782 0.7013317903851717 2.1476033624924398 chr18 78077248 40584606 0.5198006722777934 5.15092107872313 chr19 59128983 36705307 0.6207667566343903 9.988839513216345 chr20 63025520 35155019 0.5577902252928655 1.3167532709157999 chr21 48129895 21889061 0.45479137238923956 2.9293108934494896 chr22 51304566 22731032 0.44306060400160097 0.9178465836576515 chrMT 16571 4109618 248.0006034638827 75.25637884254031 chrX 155270560 76010374 0.4895350026431282 1.4986729701129522 chrY 59373566 7610522 0.1281803083884165 5.52660801828099